User: tobias.kockmann

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Posts by tobias.kockmann

<prev • 26 results • page 1 of 3 • next >
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Comment: C: how to transform a list of IRanges into a RangesList instance
... I tried to use as(..., "IRangesList") and got: Error in as(y, "IRangesList") : no method or default for coercing "list" to "IRangesList" Is there a reason why one can not coerce a list to a IRangesList? What is more specific about IRangesList objects? ...
written 6 days ago by tobias.kockmann10
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findOverlaps - how to get adjacent ranges?
... Hi there, I am trying to locate a function that finds pairs of adjacent ranges - ranges where the end of range A is exactly start-1 of range B. Example with 3 ranges: AAAAABBBBBCCCCC pair 1 AAAAA BBBBB pair 2 BBBBB CCCCC I thought that would be possible using findOverlaps() or findOverlapPairs( ...
iranges findoverlaps written 14 days ago by tobias.kockmann10 • updated 14 days ago by Michael Lawrence9.1k
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Comment: C: how to transform a list of IRanges into a RangesList instance
... THX Martin! A general question: I am starting to develop a package for dealing with peptide mapping data (data coming from a bottom-up proteomics experiment) and I think the Biostrings and IRanges package could be the basis for this, but I am having trouble to get an overview what functionality is a ...
written 5 weeks ago by tobias.kockmann10
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Comment: C: how to transform a list of IRanges into a RangesList instance
... THX! > real.rl <- as(rl, "RangesList") > class(real.rl) [1] "SimpleRangesList" attr(,"package") [1] "IRanges" Where is that function documented? ...
written 5 weeks ago by tobias.kockmann10
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how to transform a list of IRanges into a RangesList instance
... Dear bioC support, I have constructed a list of IRanges named rl: > class(rl) [1] "list" > class(rl[[1]]) [1] "IRanges" attr(,"package") [1] "IRanges" Now I realized that there is already a RangesList class in the IRanges package that I could use instead of the "primitive" list. Problem: I ...
rangeslist-class {iranges} written 5 weeks ago by tobias.kockmann10 • updated 5 weeks ago by James W. MacDonald43k
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Comment: C: Ranges on AAStrings
... I found two exceptions. findOverlaps() and countOverlaps() work directly on the Views object if queried against itself (within proteins for a AAString subject): hits <- findOverlaps(query = v1, maxgap = 1, drop.self=TRUE, drop.redundant=TRUE) c <- countOverlaps(query = v1, maxgap = 1, drop. ...
written 8 weeks ago by tobias.kockmann10
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Comment: C: Ranges on AAStrings
... True thought! ...
written 8 weeks ago by tobias.kockmann10
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Ranges on AAStrings
... Hi BioC, can anyone help me with the following: I mapped a set of peptides (short AA sequences) to a set of proteins using exact string matching. Now, I would like to compare the locations of the mapped peptide to each other, in order to find peptides that locate next to one another. To me this pr ...
biostrings aastring views written 8 weeks ago by tobias.kockmann10
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Comment: C: matching of AAStringSet vs. another AAStringSet
... Hi Herve, hmmm...I looked at the size of the list of MIndex objects returned and got this: > object.size(m[[1]]) 9458832 bytes In total the list contains 10 of these MIndex objects, so the list of MIndex objects has a total memory footprint of 90 Mb! The corresponding list-of-list structure ...
written 10 weeks ago by tobias.kockmann10
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Comment: C: matching of AAStringSet vs. another AAStringSet
... Oh really! Good to know. What are "hits objects"? The question of the return type is indeed not trivial. The list of MIndex objects returned by vmatchPattern() is not to easy to deal with...at least it is not obvious to me and it looks quite bulky (big memory footprint), because it returns an empty ...
written 10 weeks ago by tobias.kockmann10

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